Modelling toehold-mediated RNA strand displacement

TL;DR

This paper models the thermodynamics and kinetics of RNA strand displacement via toeholds using a coarse-grained approach, predicting how displacement rates depend on toehold length, position, and temperature, with implications for nanotechnology and biology.

Contribution

It introduces a coarse-grained model to study RNA toehold-mediated strand displacement, providing testable predictions on how toehold position and temperature affect reaction rates.

Findings

Displacement is faster when the toehold is at the 5' end.

Displacement rate decreases with increasing temperature for longer toeholds.

The model offers insights into RNA strand displacement mechanisms.

Abstract

We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5' end of the substrate and that the displacement slows down with increasing temperature for longer toeholds.